Recombinant HIV-1 Drawing Tool Explanation

Details

Sample InputYour data should look like the sample data below. Separate data with a space or tab.

1

2677

G

2678

3345

A

3346

3423

A/J

3424

5123

J

6000

6899

?

6900

7144

A

7145

9719

G

Sample Output
The output you would get from the data above is shown here. The actual drawing you obtain will
be larger than the one shown below, allowing you to adjust the image as needed for display or publication.

Input requirements
If you submit the data as a
file, it can be either a text file or an Excel spreadsheet (be sure to check box).
If using a text file, it should have spaces or tabs between each column and a carriage return at the end of each row.

The first column lists the start of each subtype region, the second
column the end of that region, and the third column the subtype of
that region. Each row describes the next region in the
genome. In this example, there is a precise breakpoint between
subtypes G and A at positions 2677 - 2678. If the breakpoint position is
imprecisely known, but is known to occur in a certain span, indicate
this as shown in row 3 of the table above.
The given subtype ("A/J") indicates that the breakpoint
between the A region and the downstream J region is uncertain, but
that the breakpoint occurs in this span. In the illustration, such uncertain breakpoint
regions are illustrated by an interfingering of the two
colors, and the
breakpoint in such regions is shown at the center and expresses the
size of the regions using a plus or minus notation. Don't confuse
this concept of uncertain breakpoint with a
region of uncertain or unknown subtype. The latter is indicated by
"?" or "U" (row 5) and means that that region cannot be
assigned to a known subtype. Note also that the region between 5124
and 5999 is absent in the table above, and appears uncolored in the illustration. This means no
information is available, probably because that span was not
sequenced.

If possible, breakpoints should be expressed in
HXB2
coordinates; in this case, leave the bottom two input boxes empty. If your
breakpoint data are in the coordinates of your sequence, you can
automatically convert them to HXB2 coordinates by checking the
"Non-HXB2 coordinates" checkbox and pasting in or uploading your sequence.

Subtype colors
The current default colors are as follows:

A

A1

A2

B

C

D

E

F

F1

F2

G

H

J

J1

J2

K

01

02

?

U

You can change the default colors by clikcing the 'Custom Colors' button on the tool's input page.
By doing so you will be presented with a list of your subtypes and the currently associated colors together with the
corresponding hexadecimal code. Change these colors by clicking inside that box to display a
color palette. Click on the color of your choice or type a different hex value.